Esther Lizano’s research while affiliated with Institute of Evolutionary Biology and other places

What is this page?


This page lists works of an author who doesn't have a ResearchGate profile or hasn't added the works to their profile yet. It is automatically generated from public (personal) data to further our legitimate goal of comprehensive and accurate scientific recordkeeping. If you are this author and want this page removed, please let us know.

Publications (71)


Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics
  • Article

January 2025

·

41 Reads

Genome Biology and Evolution

Ricardo Fong-Zazueta

·

Johanna Krueger

·

David M Alba

·

[...]

·

Esther Lizano

Local genetic adaptation to habitat in wild chimpanzees

January 2025

·

199 Reads

Science

How populations adapt to their environment is a fundamental question in biology. Yet, we know surprisingly little about this process, especially for endangered species, such as nonhuman great apes. Chimpanzees, our closest living relatives, are particularly notable because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether genetic adaptation facilitates such habitat diversity remains unknown, despite it having wide implications for evolutionary biology and conservation. By using newly sequenced exomes from 828 wild chimpanzees (388 postfiltering), we found evidence of fine-scale genetic adaptation to habitat, with signatures of positive selection in forest chimpanzees in the same genes underlying adaptation to malaria in humans. This work demonstrates the power of noninvasive samples to reveal genetic adaptations in endangered populations and highlights the importance of adaptive genetic diversity for chimpanzees.


Genomic diversity of the Lemuriformes
a, Heterozygosity calculated at the base-pair level from the callable genome per individual. b, Proportion of the callable genome in ROHs that are at least 500 kb in length per individual. c, Proportion of the callable genome for each wild-born individual that is in ROHs of at least 1 Mb in length plotted against the number of callable ROHs per individual. Bottom right: colour scheme for the genera within families in a and b. For the boxplots in a and b, the box corresponds to the interquartile range (IQR), the horizontal line is the median value and the length of whiskers extends up to 1.5 times the IQR. The number of individuals used to derive each boxplot (n) is listed in parentheses following the taxonomic group in the legend, and each point represents a unique individual (biological replicate).
Phylogenetic tree of Lemuriformes individuals generated from the gene trees of 3,072 UCEs reconstructed with ASTRAL
Branch lengths are in units of coalescence distance, and dotted lines extending from tree tips are only to improve visualization. The ring of colour-coded values circumscribing the tree corresponds to the heterozygosity of the corresponding individual, ranging from 0.00036 to 0.006658 het × bp⁻¹. The outlier value of M. mittermeieri (0.007754 het x bp⁻¹) is coloured independently to retain the colour scale. Individuals without values are outgroup reference assemblies from which heterozygosity values were not calculated.
Patterns of interspecific allele sharing within genera of lemuriformes
a, f4-ratio admixture proportions for each triad of species (((Species 1, Species 2), Species 3), outgroup) within each genus in our dataset that has at least three species. The significance of the f4 values was tested with a block-jackknife procedure²⁶ to produce Z-scores and FDR-adjusted P values in Dsuite. Values with FDR-corrected P values of <0.01 and Z-values of ≥2 are depicted in red. b, fb values in Lemuriformes genera. Each box indicates the amount of excess sharing of derived alleles between a species (x axis) and a branch (compared to its sister branch) on the UCE tree (y axis). The colour scale is shared across all genera and corresponds to the fb value for a given pairing. Grey boxes represent comparisons that cannot be made by Dsuite as a result of the tree topology structure.
Ecogeographic distribution and demographic history of lemurs in Madagascar
a, Species range distributions in three genera of lemurs, colour-coded by per base-pair heterozygosity in the callable genome. Species with multiple distributions in the eastern wet and northern dry forests are labelled with arrows from the centre of the island. b, Biogeographic models of species diversity in Madagascar. Left: primary ecogeographic zones of climate variation. Data from ref. ⁷⁰. Middle: centres of endemism corresponding to retreat or dispersal watersheds3,71. Right: biogeographic areas of lemur distribution. CH, central highlands region; E1, northern east region; E2, southern east region; N, north region; NW, northwest region; W1, central western region; W2, southern western region; X, Sambirano region. c, Log-transformed Ne from 1 Ma to 10 ka as reconstructed by SMC++ depicting demographic histories of Eulemur, Hapalemur and Propithecus grouped by the presence of each species in dry forest, wet forest or both. During the last 100 ka, dry-forest (dry-deciduous and sub-arid spiny forest) species follow a steep pattern of declining Ne, while those species with wet and dry distributions remain more stable. Species exclusively in the wet forest do not show a consistent pattern. Panel b, centre, adapted with permission from ref. ⁷¹, OUP. Panel b, right, adapted with permission from ref. ⁴, National Academy of Sciences.
Declining effective population sizes in lemurs and regional patterns of inbreeding across Madagascar during the last 2,000 years
a, Historical Ne in the last 2,000 years (up to 200 generations) from four lemur species reconstructed using GONE³⁰ and the Malagasy human population Ne (from ref. ⁷³). The variable time ranges of Ne plots result from the species generation times used to calculate time before present. The orange dotted line at 300 years before present indicates the rapid acceleration of anthropogenic deforestation in Madagascar. The blue dotted line at 1 ka corresponds to the beginning of human expansion and the change in lemur hunting patterns following the extinction of large-bodied subfossil species³¹. b, chronROH plots of the proportion of the callable genome per species in ROH between 300 and 2,000 years before present (BP) across endemic areas in Madagascar. In seven of nine endemic area groupings, where multiple species of lemurs are distributed, the recent temporal patterning of FROH either directly overlaps or follows a consistent pattern. An inflection point for inbreeding levels is visible at ~1 ka across multiple species and regions. Map of endemic areas adapted from previous publications3,71.
Ecological and anthropogenic effects on the genomic diversity of lemurs in Madagascar
  • Article
  • Publisher preview available

December 2024

·

283 Reads

·

1 Citation

Nature Ecology & Evolution

Ecological variation and anthropogenic landscape modification have had key roles in the diversification and extinction of mammals in Madagascar. Lemurs represent a radiation with more than 100 species, constituting roughly one-fifth of the primate order. Almost all species of lemurs are threatened with extinction, but little is known about their genetic diversity and demographic history. Here, we analyse high-coverage genome-wide resequencing data from 162 unique individuals comprising 50 species of Lemuriformes, including multiple individuals from most species. Genomic diversity varies widely across the infraorder and yet is broadly consistent among individuals within species. We show widespread introgression in multiple genera and generally high levels of genomic diversity likely resulting from allele sharing that occurred during periods of connectivity and fragmentation during climatic shifts. We find distinct patterns of demographic history in lemurs across the ecogeographic regions of Madagascar within the last million years. Within the past 2,000 years, lemurs underwent major declines in effective population size that corresponded to the timing of human population expansion in Madagascar. In multiple regions of the island, we identified chronological trajectories of inbreeding that are consistent across genera and species, suggesting localized effects of human activity. Our results show how the extraordinary diversity of these long-neglected, endangered primates has been influenced by ecological and anthropogenic factors.

View access options

Distribution of sequencing reads per library. (A) Numbers of raw reads, reads after trimming and unique reads (after BBmap clumpify) across 214 libraries. (B) Percentage of reads per library assigned to Homo, Bacteria, or Viruses using Kraken2. We note that mapping great ape sequencing data to the human genome is commonly performed in genomic studies to avoid reference bias⁶³.
Summaries of reads assigned to different virus domains and families. (A) Proportion of virus-assigned reads based on kraken2 across 214 libraries, stratified by realm and by family (for DNA viruses and Retroviridae). (B) Number of libraries with any read assigned to virus families. (C) Number of libraries with at least 25 reads assigned to virus families.
Heatmap of positive reads per viral species. The figure depicts all libraries that have at least 25 hits assigned to one of the 99 viruses in the capture kit (with merged numbers for Cytomegalovirus strains).
Maximum likelihood phylogeny of hepatitis B virus genomes obtained in this study, in the context of known viral diversity among great apes. The full HBV genomes were used, with a final SNPs alignment length of 4590 bp. The tree was rooted on a human hepatitis B strain, which serves as an outgroup. The colouring of the clades follows Fig. 3 in Locarnini et al.⁵², representing the geographical distribution of the great ape species. Samples newly sequenced in this study are marked in red.
Screening great ape museum specimens for DNA viruses

November 2024

·

117 Reads

·

1 Citation

Natural history museum collections harbour a record of wild species from the past centuries, providing a unique opportunity to study animals as well as their infectious agents. Thousands of great ape specimens are kept in these collections, and could become an important resource for studying the evolution of DNA viruses. Their genetic material is likely to be preserved in dry museum specimens, as reported previously for monkeypox virus genomes from historical orangutan specimens. Here, we screened 209 great ape museum specimens for 99 different DNA viruses, using hybridization capture coupled with short-read high-throughput sequencing. We determined the presence of multiple viruses within this dataset from historical specimens and obtained several near-complete viral genomes. In particular, we report high-coverage (> 18-fold) hepatitis B virus genomes from one gorilla and two chimpanzee individuals, which are phylogenetically placed within clades infecting the respective host species.


Sampled populations’ distribution and structure
A Sampled localities and population geographic distributions. B Principal component analysis on the black uakari dataset (n = 2.24 M SNPs). C Principal component analysis on the global dataset (n = 10.46 M SNPs). D Principal component analysis on the bald uakari dataset (n = 6.10 M SNPs).
Whole genome phylogeny phylogram
Whole genome maximum clade-credibility phylogeny from 2144 maximum likelihood trees based on 1 Mb non-overlapping sliding windows. Phylogenetic support is indicated in each split. Phylogram where branch lengths are proportional to the observed phylogenetic distance in terms of substitutions. Colors depict population labeling system, outer bar indicates bald (plum) or black (green) uakari group and bottom gray bar indicates outgroup node (Pithecia pithecia).
Demographic history of Cacajao and genetic diversity in extant populations
A Maximum likelihood model topologies and estimates for divergence times (depicted by dashed lines) and effective population sizes (depicted by color bars width, ML estimate indicated above confidence interval). Three models summarized in Fig. 3A: (i) bald and black uakaris general model, (ii) bald uakaris model and iii) black uakaris model. Bald and black ancestor Ne estimates were calculated twice: in the general model (a, c) and in the bald (b) and black (d) models respectively. B Genome-wide heterozygosity per population, points depicting individual observations and colored shape its distribution. D, dashed lines indicate mean values per group (bald: plum, black: green).
Migration patterns and gene flow in the Cacajao genus
A Estimated effective migration surfaces (EEMS) on black and bald uakaris complete dataset. Color palette depicting effective migration rate values (log(m)), where white reflects isolation by distance and color, deviations from it. B F-branch statistic on full dataset, color intensity reflecting intensity of event; significant values considered (f-branch ≥ 0.05).
Significant functional differences between bald and black uakaris
Whole genomes of Amazonian uakari monkeys reveal complex connectivity and fast differentiation driven by high environmental dynamism

October 2024

·

188 Reads

Communications Biology

Despite showing the greatest primate diversity on the planet, genomic studies on Amazonian primates show very little representation in the literature. With 48 geolocalized high coverage whole genomes from wild uakari monkeys, we present the first population-level study on platyrrhines using whole genome data. In a very restricted range of the Amazon rainforest, eight uakari species (Cacajao genus) have been described and categorized into the bald and black uakari groups, based on phenotypic and ecological differences. Despite a slight habitat overlap, we show that posterior to their split 0.92 Mya, bald and black uakaris have remained independent, without gene flow. Nowadays, these two groups present distinct genetic diversity and group-specific variation linked to pathogens. We propose differing hydrology patterns and effectiveness of geographic barriers have modulated the intra-group connectivity and structure of bald and black uakari populations. With this work we have explored the effects of the Amazon rainforest’s dynamism on wild primates’ genetics and increased the representation of platyrrhine genomes, thus opening the door to future research on the complexity and diversity of primate genomics.


Figure 1. Phylogenetic placement of the Xerces Blue. (a) Maximum likelihood tree from whole mitochondrial genomes of Xerces Blue, Silvery Blue, and Green-Underside Blue. Node labels are bootstrap support values. (b) Time-calibrated phylogeny from Bayesian inference using mitochondrial proteincoding genes of Xerces Blue and related butterflies. Node values show median age estimates from dating analysis with a molecular clock (above nodes) or from fixing the age of the root (below nodes). Bars are 95% HPD intervals for node ages. All posterior probabilities were 1, except for one node annotated in black.
Figure 5. Functional effect prediction on the fixed amino acid-changing alleles observed in Xerces Blue and Silvery Blue. (a) Wide genome Ka/Ks ratio comparison. (b) High-to-moderate effect variant comparison in homozygous sites. (c) High-to-moderate effect variant comparison in heterozygous sites. (d) Presence of high-to-moderate variants in regions of the genome in runs of homozygosity (RoH). Error bars show the standard deviation.
Coordinates of the analysed colouration genes. Genomic coordinates in G. alexis reference genomes of different wing colouration genes described in other butterfly species.
Whole genomes from the extinct Xerces Blue butterfly can help identify declining insect species

October 2024

·

184 Reads

eLife

The Xerces Blue ( Glaucopsyche xerces ) is considered to be the first butterfly to become extinct in historical times. It was notable for its chalky lavender wings with conspicuous white spots on the ventral wings. The last individuals were collected in their restricted habitat, in the dunes near the Presidio military base in San Francisco, in 1941. We sequenced the genomes of four 80- to 100-year-old Xerces Blue, and seven historical and one modern specimens of its closest relative, the Silvery Blue ( Glaucopsyche lygdamus ). We compared these to a novel annotated genome of the Green-Underside Blue ( Glaucopsyche alexis ). Phylogenetic relationships inferred from complete mitochondrial genomes indicate that Xerces Blue was a distinct species that diverged from the Silvery Blue lineage at least 850,000 years ago. Using nuclear genomes, both species experienced population growth during the Eemian interglacial period, but the Xerces Blue decreased to a very low effective population size subsequently, a trend opposite to that observed in the Silvery Blue. Runs of homozygosity and deleterious load in the former were significantly greater than in the later, suggesting a higher incidence of inbreeding. These signals of population decline observed in Xerces Blue could be used to identify and monitor other insects threatened by human activities, whose extinction patterns are still not well known.


Fig. 2. Number of genetics-only candidate SNPs. The number of candidate SNPs from the genetics-only test (bars) compared to the null expectation (white lines) at X t X* thresholds corresponding to estimated FPRs of 0.5%, 0.1% and 0.05%, for each subspecies-dataset. Note that y-axis scales are not consistent across panels.
Fig. 5. GEA candidate gene set enrichment results. Results for 0.5%, 0.1% and 0.05% FPR tails for savannah and forest candidate SNPs are shown. Vertical panels indicate results from each subspecies-dataset. Horizontal panels show the broad categories that the gene sets belong to. Multiple testing correction was done within each gene set enrichment analysis run (i.e., each tail and gene set database such as 'Pathogen-related', 'GWAS', 'Phenotype' etc.). ( A ) the number of gene sets with FDR<0.5, cells are coloured in a gradient from white (0) to red (the largest value per row) (Fig. S50 shows the numbers in each cell). ( B ) shows the FDR values for the most enriched gene sets with FDR<0.1 for at least one candidate tail in at least one subspecies-dataset ('.' FDR<0.1, '*' FDR<0.05, '**' FDR<0.01).
Local genetic adaptation to habitat in wild chimpanzees

July 2024

·

330 Reads

·

2 Citations

How populations adapt to their environment is a fundamental question in biology. Yet we know surprisingly little about this process, especially for endangered species such as non-human great apes. Chimpanzees, our closest living relatives, are particularly interesting because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether genetic adaptation facilitates such habitat diversity remains unknown, despite having wide implications for evolutionary biology and conservation. Using 828 newly generated exomes from wild chimpanzees, we find evidence of fine-scale genetic adaptation to habitat. Notably, adaptation to malaria in forest chimpanzees is mediated by the same genes underlying adaptation to malaria in humans. This work demonstrates the power of non-invasive samples to reveal genetic adaptations in endangered populations and highlights the importance of adaptive genetic diversity for chimpanzees. One-Sentence Summary Chimpanzees show evidence of local genetic adaptation to habitat, particularly to pathogens, such as malaria, in forests.


Screening great ape museum specimens for DNA viruses

April 2024

·

75 Reads

Natural history museum collections harbour a record of wild species from the past centuries, providing a unique opportunity to study animals as well as their infectious agents. Thousands of great ape specimens are kept in these collections, and could become an important resource to study the evolution of DNA viruses, whose genetic material is likely to be preserved in dry museum specimens. Here, we screened 209 great ape museum specimens for 99 different DNA viruses, using hybridization capture coupled with short-read high-throughput sequencing. We report a capture design for great ape DNA viruses, sequencing data obtained using this approach, as well as findings regarding the presence of viruses, and several viral genomes obtained from historical specimens.


Figure 4: Robinson-Foulds distances between phylogenies based on 5, 10, and 14 protein concatenation and reference species tree for maximum likelihood and Bayesian approach Spp -Reference species tree based on whole genome data (Kuderna et al. 2023), ML -maximum likelihood approach (IQ-TREE v. 1.6.12), Bay -Bayesian approach (MrBayes v.3.2.7a).
Figure 8: Robinson-Foulds distances between phylogenies based on highly conserved or variable data and reference species tree The phylogenies based on variable sites show comparably small RF-distances to the reference tree (Kuderna et al. 2023) (see Figure 4; 5 protein tree: 170, 10 protein tree: 122, 14 protein tree: 108).
Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics

February 2024

·

234 Reads

Ancient tooth enamel, and to some extent dentin and bone, contain characteristic peptides that persist for long periods of time. In particular, peptides from the enamel proteome (enamelome) have been used to reconstruct the phylogenetic relationships of fossil specimens and to estimate divergence times. However, the enamelome is based on only about 10 genes, whose protein products undergo fragmentation post mortem. Moreover, some of the enamelome genes are paralogous or may coevolve. This raises the question as to whether the enamelome provides enough information for reliable phylogenetic inference. We address these considerations on a selection of enamel-associated proteins that has been computationally predicted from genomic data from 232 primate species. We created multiple sequence alignments (MSAs) for each protein and estimated the evolutionary rate for each site and examined which sites overlap with the parts of the protein sequences that are typically isolated from fossils. Based on this, we simulated ancient data with different degrees of sequence fragmentation, followed by phylogenetic analysis. We compared these trees to a reference species tree. Up to a degree of fragmentation that is similar to that of fossil samples from 1-2 million years ago, the phylogenetic placements of most nodes at family level are consistent with the reference species tree. We found that the composition of the proteome influences the phylogenetic placement of Tarsiiformes. For the inference of molecular phylogenies based on paleoproteomic data, we recommend characterizing the evolution of the proteomes from the closest extant relatives to maximize the reliability of phylogenetic inference.


Whole-genomes from the extinct Xerces Blue butterfly reveal low diversity and long-term population decline

January 2024

·

94 Reads

The Xerces Blue (Glaucopsyche xerces) is considered to be the first butterfly to become extinct at global scale in historical times. It was notable for its chalky lavender wings with conspicuous white spots on the ventral wings. The last individuals were collected in their restricted habitat, in the dunes near the Presidio military base in San Francisco, in 1941. To explore the demographic history of this iconic butterfly and to better understand why it went extinct, we sequenced at medium coverage the genomes of four 80 to 100-year-old Xerces Blue specimens and seven historic specimens of its closest relative, the Silvery Blue (G. lygdamus). We compared these to a novel annotated genome of the Green-Underside Blue (G. alexis). Phylogenetic relationships inferred from complete mitochondrial genomes indicate that Xerces Blue was a distinct species that diverged from the Silvery Blue lineage at least 850,000 years ago. Using nuclear genomes, we show that both species experienced population growth during the MIS 7 interglacial period, but the Xerces Blue decreased to a very low effective population size subsequently, a trend opposite to that observed in the Silvery Blue. Runs of homozygosity in the Xerces Blue were significantly greater than in the Silvery Blue, suggesting a higher incidence of inbreeding. In addition, the Xerces Blue carried a higher proportion of derived, putatively deleterious amino acid-changing alleles than the Silvery Blue. These results demonstrate that the Xerces Blue experienced more than 100 thousand years of population decline, prior to its human-induced final extinction.


Citations (32)


... We repeated the phasing analysis with POOHA on the baboons sequenced in our study and those from Wu and colleagues [12], enabling us to assign 49.3% (256/519) of mutations as being transmitted by one parent or the other (Tables 2 and S3). The higher level of overall nucleotide polymorphism in baboons gave us more power to phase mutations in this species compared to aye-ayes, which have a low level of polymorphism even for strepsirrhines [25,33]. Based on the percentage of mutations that could be phased in each trio, we inferred the number of mutations that each parent transmitted to their offspring. ...

Reference:

Unprecedented female mutation bias in the aye-aye, a highly unusual lemur from Madagascar
Ecological and anthropogenic effects on the genomic diversity of lemurs in Madagascar

Nature Ecology & Evolution

... can track long-term trends in their parasite communities and even test hypotheses about drivers such as climate change 71,200,201 . Preserved tissues can also be used to discover uncharacterized pathogens, including from species that are otherwise hard to sample (for example, rare and endangered species) 202,203 (Fig. 4b). ...

Screening great ape museum specimens for DNA viruses

... In a more comprehensive manner, Fontsere et al. (2022) 39 captured chimpanzee chromosome 21 sequences from 828 noninvasive samples collected at 48 research sites, revealing four distinct subspecies with local population structures across Africa. Furthermore, a recent preprint reported that exome sequences from these 828 samples to analyze fine-scale genetic adaptation to habitat 40 . ...

Local genetic adaptation to habitat in wild chimpanzees

... We looked for variants in the 219 candidate genes in two datasets. To find aye-aye and lemuriform-specific substitutions, we extracted 239 primate species from the 447-way whole-genome multiple sequence alignments in Kuderna and colleagues [65]. Alignment data from aye-aye, 30 lemur species, and 7 sifaka species were downloaded as MAF files. ...

Identification of constrained sequence elements across 239 primate genomes

Nature

... Cave (Cortada & Maroto, 1990;, Cova del Gegant (Daura et al., 2005;Quam et al., 2015), Cova Simanya (Morales et al., 2023), Tossal de la Font (Olaria et al., 2004(Olaria et al., -2005, Cova Negra (Arsuaga et al., 2007;Richard et al., 2019), Cova Foradà (Aparicio et al., 2014;Subirà et al., 2003), El Salt (Garralda et al., 2014), Cova Bolomor (Arsuaga et al., 2001, Sima de las Palomas (Trinkaus & Walker, 2017;Walker et al., 2011Walker et al., , 2012Walker, Lombardi, et al., 2010), Boquete de Zafarraya (García Sánchez, 1986), and Gibraltar Caves (Bokelmann et al., 2019;Finlayson et al., 2006). The sites of Cova Bolomor dated around 120 kyr BP, and Sima de las Palomas, dated between 128 and 60 kyr BP, have yielded some of the oldest Neanderthal remains of the Iberian Peninsula (Arsuaga et al., 2001Walker et al., 2011Walker et al., , 2012Walker, Lombardi, et al., 2010). ...

A new assemblage of late Neanderthal remains from Cova Simanya (NE Iberia)

... Using these methods, it is possible to determine whether populations have suffered the deleterious effects of population declines and to assess the need for and feasibility of specific measures to restore their level of diversity, for example, using genetic rescue (Frankham, 2015). These methods have also been used to investigate the genomic signals of population decline leading to the extinction of the Xerces Blue butterfly, Glaucopsyche xerces (De-Dios et al., 2023). Screening for such signals might be very useful to detect and prevent future extinctions. ...

Whole-genomes from the extinct Xerces Blue butterfly can help identify declining insect species

... These traits could be used to identify other remains belonging to P. capensis, but a revision of the southern African paleoanthropological assemblages would be needed beforehand as it is too premature to formally assign other specimens to the hypodigm for now. However, a recent paleoproteomic analysis revealed a high degree of morphological and proteomic variation among four Paranthropus dental specimens from the 2-Ma Member 1 of Swartkrans, suggesting based on the absence of AMELY proteins that some of the largest teeth likely belong to female individuals, whereas smaller ones (like SK 835) are males and hinting at the possible presence of two species within the sample (Madupe et al., 2023). The M 3 SK 835 shows smaller dimensions (Dean et al., 2020) and a different shape of the EDJ than most specimens from Swartkrans and TM 1517, the holotype of P. robustus. ...

Enamel proteins reveal biological sex and 1 genetic variability within southern African 2 Paranthropus

... AI models like AlphaMissense and PrimateAI-3D have demonstrated remarkable capabilities in predicting the pathogenicity of genetic variants based on structure and function of proteins and evolutionary conservation [33,34]. AlphaMissense is a deep learning model that leverages protein structural information and evolutionary constraints from related sequences to accurately classify genetic variants as benign or pathogenic [33]. ...

The landscape of tolerated genetic variation in humans and primates
  • Citing Article
  • June 2023

Science

... Ayeayes also have a long life span relative to their body size, in some cases living more than 30 years and reproducing at much older ages than other lemuriforms [23]. Their distinctive morphology and behavior have evolved through an extensive period of evolutionary independence: D. madagascariensis is the only extant member of the Daubentoniidae primate family and is estimated to have diverged from all other Malagasy lemurs at least 50 million years ago [24,25]. ...

A global catalog of whole-genome diversity from 233 primate species
  • Citing Article
  • June 2023

Science